Research workbench
Structural characterization for the nucleotide binding ability of subunit a of the A1AO ATP synthase
Analyse Structural characterization for the nucleotide binding ability of subunit a of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ND8
- Type
- protein
- Length
- 510 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V-type ATP synthase alpha chain
- EC
- 3.6.3.14
- UniProt
- O57728
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | V-type ATP synthase alpha chain (EC 3.6.3.14) | protein | 510 | 36% helix, 21% strand | O57728 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 4 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.69 | 0.97 | 16 | empty |
| 2 | 497 | 0.69 | 0.79 | 59 | empty |
| 3 | 107 | 0.55 | 0.84 | 24 | empty |
| 4 | 120 | 0.51 | 0.81 | 22 | MRD |
| 5 | 51 | 0.38 | 0.81 | 20 | empty |
Compared structures
- 3ND8 · Structural characterization for the nucleotide binding ability of subunit A of the A1AO… · the same entry in another collection · chain A against A, TM-score 1.00
- O57728 · AlphaFold monomer V2.0 prediction for V-type ATP synthase alpha chain (O57728) · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O57728
- Elsewhere: RCSB PDB 3ND8 · PDBe 3ND8 · UniProt O57728
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